Scene authoring tools: Difference between revisions
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===add to or remove from selection=== | ===add to or remove from selection=== | ||
This is the main tool for creating selections. This box allows you to specify groups of atoms to either ADD to the current selection, or REMOVE from the current selection. It is advised to either begin with ALL atoms selected and then use this box to REMOVE atoms to your selection to arrive at your desired selection, or alternatively to begin with NO atoms selected and then use this box to ADD atoms to your selection to arrive at your desired selection. | This is the main tool for creating selections. This box allows you to specify groups of atoms to either ADD to the current selection, or REMOVE from the current selection. It is advised to either begin with ALL atoms selected and then use this box to REMOVE atoms to your selection to arrive at your desired selection, or alternatively to begin with NO atoms selected and then use this box to ADD atoms to your selection to arrive at your desired selection. | ||
It is advised that you use selection halos while creating a selection so that you may view the atoms that your selection comprises. | |||
Each input box allows you to specify certain parameters in order to best choose what to add or remove to/from your selection. There is an imaginary 'AND' (or intersection) connecting each input box (a Boolean AND), but an 'OR' (or union) connecting the chosen elements within each input box. What this means is that if you choose in the 'groups' box the items 'all protein' and 'dna' and in the 'limit to elements' box you type in 'C,O' and click "add to selection", then you will add to your selection all the carbon and oxygen atoms that are part of either the protein or the dna in your loaded file (it's like saying "(all protein OR dna) AND (carbon OR oxygen)" ) | Each input box allows you to specify certain parameters in order to best choose what to add or remove to/from your selection. There is an imaginary 'AND' (or intersection) connecting each input box (a Boolean AND), but an 'OR' (or union) connecting the chosen elements within each input box. What this means is that if you choose in the 'groups' box the items 'all protein' and 'dna' and in the 'limit to elements' box you type in 'C,O' and click "add to selection", then you will add to your selection all the carbon and oxygen atoms that are part of either the protein or the dna in your loaded file (it's like saying "(all protein OR dna) AND (carbon OR oxygen)" ) | ||
The 'groups' box lists various pre-defined groups of atoms by name. The 'limit to chains' box allows you to choose specific chains by the names they are given in the loaded file (ex: A,C,D). The 'limit to resi types' allows specification of residues by their 3-letter codes (ex: PHE,ALA,GLY). The 'limit to residue nos' box allows specification of residues by their number (ex: 18,23-25,32). The 'limit to elements' box allows choosing specific elements or even specific isotopes (ex: Fe,2H,31P). The 'limit to atom nos' box allows specifying atoms by their number. The 'sites' box appears only if your file is a PDB file that has predefined sites that the authors defined when they submitted the file to the Protein Data Bank. | The 'groups' box lists various pre-defined groups of atoms by name. The 'limit to chains' box allows you to choose specific chains by the names they are given in the loaded file (ex: A,C,D). The 'limit to resi types' allows specification of residues by their 3-letter codes (ex: PHE,ALA,GLY). The 'limit to residue nos' box allows specification of residues by their number (ex: 18,23-25,32). The 'limit to elements' box allows choosing specific elements or even specific isotopes (ex: Fe,2H,31P). The 'limit to atom nos' box allows specifying atoms by their number. The 'sites' box appears only if your file is a PDB file that has predefined sites that the authors defined when they submitted the file to the Protein Data Bank. | ||
The button 'add to selection' checks the information that was specified by you in the boxes in the 'add to or remove from selection' area and then adds what you specified into the current selection. The 'remove from selection' does the same, but rather than adding to the current selection, it removes from the current selection. | |||
===select within distance=== | |||
Here you may enter a value (in Angstroms) and press 'go'. Any atom within a distance from the current selection equal to or smaller than the the number of Angstroms you specifed will be added to the selection. To clarify, an example: If you had a ligand selected, and then inputted 5 and hit 'go', then all atoms within 5 Angstroms of that ligand would be added to your selection. Your selection would then be composed of the ligand as well as all atoms within 5 Angstroms of it. | |||
===mouse click selects=== | |||
Choosing 'default' sets it so that mouse clicks on the Jmol applet are set to their defualt setting in Jmol. In the default setting, clicking does not select or deselect any atoms, but clicking to create measurements is enabled. Choosing 'center' makes it so that any click on an atom, centers both the view and the axis of rotation on the atom. Choosing 'atom' is perhaps the most useful setting for creating selections as each click on an atom either adds it to the selection, or if it is already part of the selection, removes it from the selection. Choosing 'element' makes it so that clicking on an atom will select all other atoms of the same element. Choosing 'molecule' makes it so that clicking on an atom selects all other atoms of the same molecule. | |||
=='representations' tab== | |||
The first area is the 'all and halo toggle' area. This provides a button to select all atoms, and a checkbox to turn selection halos on or off. | |||
The 'set selection representation' box provides a variety of choices for setting the representation of the current selection. Multiple representations can be turned on for the same selection of atoms (for instance using both wireframe and spacefill can create a 'ball and stick' scheme). Click on the representations that you would like to turn on for your current selection and then press 'set representation'. Every representation that has been checked off (to the left of the representation's name) will be displayed. Some representations have an input field to their direct right. If they do, then you may enter values in order to change the form of the representation, usually its size. If you leave the input field blank, the default will be used. | |||
Clicking on 'hide selection' turns off all representations for the selection. | |||
=='colors' tab== | |||
==Manipulating Jmol with your mouse== | ==Manipulating Jmol with your mouse== | ||